1F23 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CONTRIBUTION OF A BURIED HYDROGEN BOND TO HIV-1 ENVELOPE GLYCOPROTEIN STRUCTURE AND FUNCTION

Authors :   J. Liu, W. Shu, M. Fagan, J. H. Nunberg, M. Lu

Date :   23 May 00 (Deposition) - 20 Jun 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Hiv-1 Envelope Protein, Gp41, Membrane Fusion, Hiv-1 Entry, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Liu, W. Shu, M. B. Fagan, J. H. Nunberg, M. Lu
Structural And Functional Analysis Of The Hiv Gp41 Core Containing An Ile573 To Thr Substitution: Implications For Membrane Fusion.
Biochemistry V. 40 2797 2001
PubMed-ID: 11258890 | Reference-DOI: 10.1021/BI0024759
(for further references see the PDB file header)

Molecule 1 - TRANSMEMBRANE GLYCOPROTEIN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PN36(L)C34
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	ECTODOMAIN
	Mutation	:	YES
	Organism Scientific	:	HUMAN IMMUNODEFICIENCY VIRUS 1
	Organism Taxid	:	11676
	Synonym	:	GP41

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1F23)

(no "Site" information available for 1F23)

(no "SS Bond" information available for 1F23)

(no "Cis Peptide Bond" information available for 1F23)

(no "SAP(SNP)/Variant" information available for 1F23)

(no "PROSITE Motif" information available for 1F23)

(no "Exon" information available for 1F23)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:74
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:115
                                   551       561       571       581       591       601       611       621       631       641       651     
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL 656
               SCOP domains d1f23a_ A: Retrovius gp41 protease -resi             st                           ant core                          SCOP domains
               CATH domains 1f23A00 A:1-75  [code=1.10.287.210 , no              na                           me defined]                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-.....-------------..---------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 A   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQAR-LSGGR-------------GG---------------------------WMEWDREINNYTSLIHSLIEESQNQQEKNEQEL  75
                                    10        20        30   | |  40         -   ||    -         -         -  |     50        60        70     
                                                            34 |  40            41|                          43                                
                                                              36                 42

Chain B from PDB  Type:PROTEIN  Length:72
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:116
                                   551       561       571       581       591       601       611       621       631       641       651      
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL 657
               SCOP domains d1f23b_ B: Retrovius gp41 protease-                                            resistant core                        SCOP domains
               CATH domains 1f23B00 B:1-76  [code=1.10.287.210,                                             no name defined]                     CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..--------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 B   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQARI--------------------------------------------RGGWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL  76
                                    10        20        30    |    -         -         -         -        40        50        60        70      
                                                             35                                           40

Chain C from PDB  Type:PROTEIN  Length:71
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:115
                                   551       561       571       581       591       601       611       621       631       641       651     
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL 656
               SCOP domains d1f23c_ C: Retrovius gp41 protease-                                            resistant core                       SCOP domains
               CATH domains 1f23C00 C:1-75  [code=1.10.287.210,                                             no name defined]                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.--------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 C   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQARI--------------------------------------------RGGWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL  75
                                    10        20        30    |    -         -         -         -        40        50        60        70     
                                                             35                                           40

Chain D from PDB  Type:PROTEIN  Length:75
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:115
                                   551       561       571       581       591       601       611       621       631       641       651     
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL 656
               SCOP domains d1f23d_ D: Retrovius gp41 protease-r                 es                       istant core                           SCOP domains
               CATH domains 1f23D00 D:1-75  [code=1.10.287.210,                  no                        name defined]                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------..-----------------------.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 D   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQARIL-----------------SG-----------------------GRGGWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL  75
                                    10        20        30     |   -         -   ||    -         -        40        50        60        70     
                                                              36                37|                      39                                    
                                                                                 38

Chain E from PDB  Type:PROTEIN  Length:75
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:115
                                   551       561       571       581       591       601       611       621       631       641       651     
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL 656
               SCOP domains d1f23e_ E: Retrovius gp41 protease-r                 es                       istant core                           SCOP domains
               CATH domains 1f23E00 E:1-75  [code=1.10.287.210,                  no                        name defined]                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh-----------------..-----------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 E   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQARIL-----------------SG-----------------------GRGGWMEWDREINNYTSLIHSLIEESQNQQEKNEQEL  75
                                    10        20        30     |   -         -   ||    -         -        40        50        60        70     
                                                              36                37|                      39                                    
                                                                                 38

Chain F from PDB  Type:PROTEIN  Length:73
 aligned with Q89797_9HIV1 | Q89797 from UniProtKB/TrEMBL  Length:852

    Alignment length:116
                                   551       561       571       581       591       601       611       621       631       641       651      
         Q89797_9HIV1   542 SGIVQQQNNLLRAIEAQQHLLQLTVWGIKQLQARILAVDRYLKDQQLLGIWGCSGKLICTTAVPWNDSWSNKTLEQIWNRTTWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL 657
               SCOP domains d1f23f_ F: Retrovius gp41 protease-r                                           esistant core                         SCOP domains
               CATH domains 1f23F00 F:1-76  [code=1.10.287.210,                                            no name defined]                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.-------------------------------------------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 1f23 F   1 SGIVQQQNNLLRAIEAQQHLLQLTVWGTKQLQARIL-------------------------------------------RGGWMEWDREINNYTSLIHSLIEESQNQQEKNEQELL  76
                                    10        20        30     |   -         -         -         -        40        50        60        70      
                                                              36                                          40

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Coiled coil proteins (689)

Fold: Stalk segment of viral fusion proteins (231)

Superfamily: Virus ectodomain (48)

Family: Virus ectodomain (44)

Protein domain: Retrovius gp41 protease-resistant core (35)

Human immunodeficiency virus type 1 [TaxId: 11676] (23)

1a	d1f23a_	A:
1b	d1f23b_	B:
1c	d1f23c_	C:
1d	d1f23d_	D:
1e	d1f23e_	E:
1f	d1f23f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: [code=1.10.287.210, no name defined] (35)

Human immunodeficiency virus 1. Organism_taxid: 11676. (9)

1a	1f23D00	D:1-75
1b	1f23E00	E:1-75
1c	1f23A00	A:1-75
1d	1f23F00	F:1-76
1e	1f23B00	B:1-76
1f	1f23C00	C:1-75

(no "Pfam Domain" information available for 1F23)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (Q89797_9HIV1 | Q89797)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0039663	membrane fusion involved in viral entry into host cell	Merging of the virion membrane and a host membrane (host plasma membrane or host organelle membrane) that is involved in the uptake of a virus into a host cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0044174	host cell endosome	A membrane-bounded organelle that carries materials newly ingested by endocytosis. It passes many of the materials to host cell lysosomes for degradation.
	GO:0044175	host cell endosome membrane	The lipid bilayer surrounding a host cell endosome.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0019031	viral envelope	The lipid bilayer of a virion that surrounds the protein capsid. May also contain glycoproteins.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.
	GO:0055036	virion membrane	The lipid bilayer surrounding a virion.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 1f23)

	Sites
(no "Sites" information available for 1f23)

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1f23)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1f23
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	Q89797_9HIV1 \| Q89797
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	Q89797_9HIV1 \| Q89797
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1F23)

(no "Related Entries Specified in the PDB File" available for 1F23)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (1, 6)

Pfam Domains (0, 0)

Gene Ontology (14, 14)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File